Smith topped the run aggregate for Australians across the three global formats, but his Test form was the most impressive - 1305 runs in 11 matches at an average of 81.56, with six centuries.
Smith, who had earlier been named Australia's Test Player of the Year for his dominant 12 months with the bat, won his first Border Medal in 2015.
Skipper Steve Smith was on Monday crowned the 2018 Allan Border medallist for the second time, besides grabbing Cricket Australia's Test Player of the Year award for his sensational run in the five-day format, including guiding the Kangaroos to regain the Ashes urn.
Steve Smith and Ellyse Perry have dominated the major awards at Australian cricket's Allan Border Medal night. Warner received 162 votes, while spinner Nathan Lyon and pace bowler Pat Cummins got 156 and 111 votes respectively.
He was recently named ICC Test Cricketer of the Year as well for scoring 1,875 runs, which included eight hundreds and five half-centuries, in 16 matches at an average of 78.12.
Meanwhile, Ellyse Perry won the Belinda Clark Award for her fine showing previous year with the double century in the historic Day-Night Ashes Test being the highlight. The left-hander garnered 24 votes to win the award by a margin of six from Steve Smith and all-rounder Marcus Stoinis.
Aaron Finch claimed the T20 International Player of the Year, edging out Adam Zampa by one vote.
The votes from the three formats were weighted for the Border Medal.
George Bailey and Mooney were named the top domestic players, while Jhye Richardson won the Bradman men's young player category and Georgia Redmayne took out the Betty Wilson young women's player honour. Bailey scored 1,468 runs at a combined average of 52.43.
Meanwhile, former Australia captains Ricky Ponting and Karen Rolton, along with batsman Norm O'Neill, were inducted into the Australian Cricket Hall of Fame.